Search Results (126)

Chromosome rearrangements during plant evolution can lead to alterations in genome structure and gene function, thereby influencing species adaptation and evolutionary processes. Gymnosperms, as an ancient group of plants, offer valuable insights into the morphological, physiological, and ecological characteristics of early terrestrial flora. The reconstruction of ancestral karyotypes in gymnosperms may provide critical clues for understanding their evolutionary history. In this study, we inferred the ancestral gymnosperm karyotype (AGK), which comprises 12 chromosomes, and conducted a collinearity analysis with existing gymnosperm genomes. Our findings indicate that chromosome numbers have remained remarkably stable throughout the evolution of gymnosperms. For species with multiplied chromosome numbers, such as gnetophytes, weak collinearities with the AGK were observed. Comparisons between the AGK and gnetophyte genomes revealed a biased pattern regarding retained duplication blocks. Furthermore, our analysis of transposable elements in Welwitschia mirabilis identified enriched regions containing LINE-1 retrotransposons within the syntenic blocks. Syntenic analysis between the AGK and angiosperms also demonstrated a biased distribution across chromosomes. These results provide a fundamental resource for further characterization of chromosomal evolution in gymnosperms. Full article

Diptera comprises more than 154,000 described species, representing approximately 10–12% of insects. Members have successfully colonized all continents and a wide range of habitats. However, higher-level phylogenetic relationships within Diptera have remained ambiguous. Mitochondrial genomes (mitogenomes) have been used as valuable molecular markers for resolving phylogenetic issues. To explore the effect of such markers in solving the higher-level phylogenetic relationship of Diptera, we sequenced and annotated the mitogenomes of 25 species, combined with 180 mitogenomes from 33 superfamilies of dipteran insects to conduct a phylogenetic analysis based on the PCGsrRNA and PCGs12rRNA datasets using IQ-TREE under the partition model. The phylogenetic analysis failed to recover the monophyly of the two suborders Nematocera and Brachycera. Two of six infraorders within the Nematocera—Tipulomorpha and Ptychopteromorpha—were monophyletic. The ancestral Deuterophlebiidae were a strongly supported sister group of all remaining Diptera, but Anisopodidae, as the closest relative of Brachycera, received only weak support. Three of four infraorders within Branchycera—Tabanomorpha, Xylophagomorpha, and Stratiomyomorpha—were, respectively, supported as a monophyletic clade, except Muscomorpha due to the strong long-branch attraction between Cecidomyiidae and Nycteribiidae. The inferred infraordinal relationships followed the topology Tabanomorpha + (Xylophagomorpha + (Stratiomyomorpha + Muscomorpha)). However, the proposed topology lacks strong statistical support, suggesting alternative relationships remain plausible. Based on mitogenome data alone, we infer that Diptera originated earlier than the Late Triassic at 223.43 Mya (95% highest posterior density [HPD] 166.60–272.02 Mya) and the earliest brachyeran Diptera originated in the mid-Jurassic (171.61 Mya). Full article

Genome-wide association studies (GWASs) play a central role in precision medicine, powering a range of clinical applications from pharmacogenomics to disease risk prediction. A critical component of GWASs is genotype imputation, a computational method used to infer untyped genetic variants. While imputation increases variant coverage by estimating genotypes at untyped loci, this expanded coverage can enhance the ability to detect genetic associations in some cases. However, imputation also introduces biases, particularly for rare variants and underrepresented populations, which may compromise clinical accuracy. This review examines the challenges and clinical implications of genotype imputation errors, including their impact on therapeutic decisions and predictive models, like polygenic risk scores (PRSs). In particular, the sources of imputation errors have been deeply explored, emphasizing the disparities in performance across ancestral populations and downstream effects on healthcare equity and addressing ethical considerations surrounding the access to equitable genomic resources. Based on the above, we propose evidence-based best practices for clinical GWAS implementation, including the direct genotyping of clinically actionable variants, the cross-population validation of imputation models, the transparent reporting of imputation quality metrics, and the use of ancestry-matched reference panels. As genomic data becomes increasingly adopted in healthcare systems worldwide, ensuring the accuracy and inclusivity of GWAS-derived insights is paramount. Here, we suggest a framework for the responsible clinical integration of imputed genetic data, paving the way for more reliable and equitable personalized medicine. Full article

Perkinsiodendron macgregorii, an endangered Chinese endemic tree with high ornamental and ecological value, faces extinction threats due to its poor natural regeneration and habitat degradation. Despite the urgent need for its conservation, the genetic architecture and population differentiation mechanisms of this taxon remain poorly understood, hindering science-based protection strategies. We conducted comprehensive chloroplast genomic analyses of 134 individuals from 13 natural populations to inform science-based conservation. The chloroplast genome (158,538–158,641 bp) exhibited conserved quadripartite organization, with 113 functional genes and elevated GC contents in IR regions (42.99–43.02%). Population-level screening identified 741 SNPs and 678 indels, predominantly in non-coding regions (89.8%), with three distinct phylogeographic clades revealing north-to-south genetic stratification. The northern clade (Clade A) demonstrates the highest haplotype diversity and nucleotide diversity, followed by the southern clade (Clade C), while the central clade (Clade B) exhibits signals of genetic erosion (Tajima’s D > 3.43). Based on the genetic diversity distribution and phylogenetic tree of extant P. macgregorii, we inferred that the northern populations represent ancestral groups, while the Wuyi Mountains region and Nanling Mountains region served as glacial refugia. It is imperative to implement in situ conservation in these two regions. Additionally, ex situ conservation should involve collecting seed from representative populations across all three clades and establishing isolated cultivation lines for each clade. These findings establish a genomic framework for conserving endangered plants. Full article

The majority of native cattle in the central region of China are taurine × indicine cattle with diverse phenotypes. Zaosheng cattle, a native Chinese breed from Gansu Province, exhibit excellent meat quality and good adaptability. This cattle breed is still in the development phase from a drought type to a beef breed. To further study Zaosheng cattle, we used whole-genome sequencing data from 19 Zaosheng cattle samples and 91 published samples to understand their genetic diversity, population structure, and environmental adaptation. We provided a comprehensive overview of the sequence variation to explore the genetic changes in Zaosheng cattle due to environmental adaptation. According to genetic composition analysis, this study demonstrated that Zaosheng cattle are derived primarily from East Asian indicine cattle and East Asian cattle; specifically, Zaosheng and Qinchuan cattle are the most genetically similar. Through ancestral fragment inference and selective sweep analysis, we identified several genes linked to lipid metabolism, immune regulation, fertility, and meat quality across the mosaic genome of Zaosheng cattle, revealing numerous indicators of taurine or indicine ancestry. In summary, this study provides essential genetic insights into the genome diversity of Zaosheng cattle, while establishing a foundation for conserving their genetic resources and improving crossbreeding. Full article

A new method of macroevolutionary analysis—high-resolution phylogenetics, integrating both morphological and molecular traits—has revealed well-supported evidence of complexity-based processes generating and controlling biodiversity. A novel technique of using evolutionary rates following a strict morphological clock, at least approximately, may allow detailed information on speciation and extinction events across geologic time. Branching series of minimally monophyletic genera are used to characterize in detail the branching lineage of the widely distributed moss family Streptotrichaceae. A strict morphological clock is calibrated by timing of genera new to recently exposed islands, molecular scaling against fossil taxa, and fossil evidence of the origin of the modern bryoflora. The numbers of genera generated in each 22-million-year interval are similar, while only one genus is inferred as extinct. The general outline of the phylogeny is tadpole-shaped because cumulative extinction is less than cumulative speciation, thus sustaining the family over vast time spans. Extant species per genus increase significantly over time, not through the proliferation of secondary descendants (i.e., more than four species per ancestral node), but through the selective preservation of lineages via extinction. Ancient traits are preserved throughout the lineage. It is hypothesized that descendant species are protected from coeval competition through bursts of speciation. This study supports a complexity-based explanation of the interaction of major evolutionary processes resulting in sustainability. Full article

Psectrocladius, a genus within the species-rich subfamily Orthocladiinae (Diptera: Chironomidae), remains poorly resolved in molecular phylogenetics due to limited available molecular data. Here, we sequenced and analyzed the complete mitogenomes of five Psectrocladius species, using two Rheocricotopus species as outgroups. Our results reveal that the mitogenomes of Psectrocladius are structurally conserved and retain a presumed ancestral gene order. The nucleotide composition of these newly generated mitogenomes exhibits a pronounced A + T bias, which is characteristic of typical insect mitogenomes. The substitution rates, estimated using Ka/Ks ratios, indicate that all protein-coding genes are under purifying selection. The strongest purifying selection pressure was observed in the CO1 gene, while the weakest was in the ND5 gene. Both the maximum likelihood and Bayesian inference trees consistently show the following topology: ((((P. schlienzi + P. bisetus) + P. barbimanus) + P. oligosetus) + P. aquatronus). This study provides key insights into chironomid mitogenomes and their gene properties, offering valuable reference data for future research. Full article

Background: The Satyrinae subfamily represents a taxonomically critical group within Nymphalidae, characterized by its remarkable species diversity. Despite its evolutionary significance, the phylogenetic relationships among tribal and subtribal lineages remain poorly resolved. Although mitochondrial genomes have become crucial molecular markers in Lepidoptera phylogenetics, their potential remains underutilized in the systematics of Satyrinae. Notably, Amathusiini exhibits a particular paucity, with only two congeneric representatives having been comprehensively sequenced to date. Methods: We employed high-throughput sequencing to assemble the complete mitochondrial genomes of two Amathusiini species, Discophora sondaica and Aemona amathusia. Our study revealed novel evolutionary insights through comparative genomics, which encompassed all available Satyrinae mitochondrial genomes. Additionally, we conducted phylogenetic reconstruction using maximum likelihood and Bayesian inference approaches, utilizing the most extensive dataset to date. Results: The closed, circular mitochondrial genomes measure 15,333 bp for D. sondaica and 15,423 bp for A. amathusia, maintaining the ancestral lepidopteran architecture: 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and an AT-rich control region. Comparative analyses of 71 mitochondrial genomes revealed strong evolutionary conservation across multiple parameters: nucleotide composition (AT content range: 77.9–81.8%), codon usage bias (ENC = 30.83–37.55), tRNA secondary structures, and control region organization. All PCGs showed purifying selection signals (Ka/Ks < 1.0), with atp8 exhibiting the highest evolutionary rate (Ka/Ks = 0.277). Phylogenetic reconstructions yielded congruent tribal-level topologies with strong nodal support: ((Satyrini + Melanitini) + (Amathusiini + Elymniini) + Zetherini), confirming a sister relationship between Amathusiini and Elymniini. Within Satyrini, five subtribes formed monophyletic groups: Ypthimina, Erebiina, Maniolina, Satyrina, and Melanargiina, arranged as ((Ypthimina + (Erebiina + Maniolina)) + (Satyrina + Melanargiina)). Mycalesina, Lethina, and Parargina comprised a well-supported clade (BS = 100%; PP = 1.0), though internal relationships required further resolution due to Lethina’s polyphyly. Conclusions: This study provides novel insights into mitochondrial genomic evolution within the Satyrinae subfamily while elucidating the efficacy of mitogenomic data for resolving deep phylogenetic relationships within this ecologically significant subfamily. Our findings establish critical genome baselines for further systematic research and underscore essential pathways for refining subtribal-level taxonomy through integrative molecular approaches. Full article

Banisteriopsis is a genus in the Malpighiaceae family with 61 species, notable for including ritualistic taxa such as B. caapi (Spruce ex Griseb.) C.V. Morton, one of the main components of Ayahuasca tea. We analyzed 38 Banisteriopsis species, representing more than 60% of the genus, to investigate its geographical origin, diversification period, and colonization routes in the Neotropics. Plastid genes (matK, ndhF, and rbcL) and nuclear regions (ETS, ITS, and PHYC) were used in our analyses. Divergence time analyses were performed using Bayesian inference with a relaxed molecular clock and ancestral area reconstruction. Our results show that Banisteriopsis originated in the Miocene approximately 22 million years ago, and its diversification coincides with the expansion of dry areas in South America. Banisteriopsis began colonizing the Cerrado earlier than most other plants, and the history of the genus reveals that the biome served as a source of species for Neotropical rainforests. Our results also indicate a probable ancient origin for B. caapi, with no evidence of human manipulation in its diversification, and they reinforce archaeological evidence of a millennia-old exchange of uses among Amazonian peoples. Full article

The genus Cyprinus encompasses economically vital freshwater fish species; yet the phylogenetic relationships and evolutionary history of many taxa within this genus remain unresolved. To address this knowledge gap, we reconstructed the molecular phylogenetic and estimated divergence times using complete mitochondrial cytochrome b (CYTB) sequences of 76 Cyprinidae specimens, within Cyprinidae, including 4 outgroup species. Phylogenetic trees were reconstructed using maximum likelihood (ML) and Bayesian inference (BI) methods, while divergence times were estimated using a Bayesian relaxed molecular clock approach. The results confirmed the monophyly of the genus Cyprinus. The relationships among C. (Cyprinus) multitaeniata, C. (C.) pellegrini, C. (C.) acutidorsalis, and three Erhai Lake species (C. (C.) longipectoralis, C. (C.) barbatus, and C. (C.) chilia) were resolved with strong support. Cyprinus (C.) multitaeniata is basal. The species in Erhai Lake form a monophyletic group, and C. (C.) acutidorsalis is at the top of the phylogenetic tree. The taxonomic delineation within the genus Cyprinus remains controversial, particularly regarding the proposed division into two subgenera (Cyprinus and Mesocyprinus), which has been historically constrained by limited specimen availability for Mesocyprinus. Our comprehensive phylogenetic analysis reveals significant evolutionary divergence patterns: The genus Cyprinus diverged from Carassius during the 56.9 Mya. Notably, the Erhai Lake radiation species (C. (C.) longipectoralis, C. (C.) barbatus, and C. (C.) chilia) originated during 2.03 Mya, while the Lake Biwa endemic C. (C.) haematopterus demonstrates 8.7 Mya. We identified a late Pleistocene speciation event (0.75 Mya) in C. (C.) acutidorsalis, coinciding with its adaptation to brackish water ecosystems. The native C. (C.) pellegrini of Xingyun Lake and Chilu Lake may have originated 4.8 Mya, when the ancient lake that its ancestral population inhabited became isolated. These findings provide robust molecular evidence supporting the recognition of two evolutionary distinct subgenera within Cyprinus. Full article

Brachyura is among the most diverse groups of crustaceans, with over 7000 described species. Crab mitogenomes are important for understanding molecular evolution and phylogenetic relationships. Grapsus albolineatus exhibits specific rearrangements compared with the Pancrustacean ground pattern and other Brachyura species. The gene arrangement of G. albolineatus is similar to that of ancestral crustaceans, barring that of the translocated trnH gene. In phylogenetic analyses, the Bayesian inference estimation was observed to be superior to the maximum likelihood estimation when the nodal support values were compared. Considering the results of the gene rearrangement pattern and phylogenetic analysis, we speculate that G. albolineatus belongs to Grapsidae. Our comparative study indicated that mitogenomes are a useful phylogenetic tool at the subfamily level within Brachyura. The findings indicate that mitogenomes could be a useful tool for systematics in other Brachyuran species. Full article

The arrival of psittacine in North America is well known but undefined. It is widely accepted that these birds originated in South America, and it has been suggested that different factors have promoted the biodiversity of birds in Mexico. However, in general, for North American psittacine, there are no proposed divergence times, and the possible influence of different geological events on these processes is unknown. In this study, phylogenetic relationships, divergence times, and ancestral areas of the genera Aratinga, Eupsittula, and Psittacara and related genera were estimated to propose hypotheses of the origin, diversification, and dispersal of groups under a Bayesian inference framework based on mitochondrial molecular markers. Of seven monophyletic clades within the Arini tribe, four coincided with the genera Psittacara, Eupsittula, Rhynchopsitta, and Pyrrhura, while Aratinga was grouped with Conuropsis and Cyanopsitta. Diversification of the analyzed genera probably occurred during the Miocene and around the Miocene–Pliocene boundary. The results suggest that the most likely origin of these genera is the Amazonian or Chaco regions. The diversification of these groups seems to be related to geoclimatic events associated with the uplift of the central and northern portions of the Andes and the closure of the Isthmus of Panama. We propose routes from south to north in the Neotropics and the use of the Greater and Lesser Antilles as a northward path. Full article

This study characterizes the evolution of the tumor necrosis factor superfamily (TNFSF) across vertebrate lineages, both cyclostomes and gnathostomes, by combining sequence similarity and synteny data for the genes from 23 model species. The available evidence supports a simple model in which most of the diversity found in living species can be attributed to the expansion of four genes found in an ancestor of all vertebrates before the first of the genome duplications that occurred in the vertebrate lineages. It is inferred that the ancestor of all cyclostomes possessed only six TNFSF genes. A cyclostome-specific genome triplication had little effect on the total number of these genes. The ancestor of all gnathostomes, due to the effect of a second genome duplication plus additional single-gene duplications, already had 21 TNFSF genes. In several gnathostome lineages, particularly in some tetrapods, the TNF superfamily has significantly contracted due to numerous gene losses. This evolutionary model provides a framework for exploring functional data, showing that the descendants of different ancestral genes have acquired distinct roles, most prominently in the innate and adaptive immune systems, which led to a species-specific refinement of which TNFSF genes were conserved or lost. Several data hitherto difficult to interpret (the interactions of very different TNFSF ligands with the same receptors; the ability of the same ligands to bind alternative receptors, with or without death domains; and the cooperation of different ligands in specific functions) can be explained as consequences of the evolutionary history of the TNF superfamily. Full article

The Cordycipitaceae family of insecticidal fungi is widely distributed in nature, is the most complex in the order Hypocreales (Ascomycota), with members displaying a diversity of morphological characteristics and insect host ranges. Based on Bayesian evolutionary analysis of five genomic loci(the small subunit of ribosomal RNA (SSU) gene, the large subunit of ribosomal RNA (LSU) gene, the translation elongation factor 1-α (tef1-α) gene, the largest subunit of RNA polymerase II (rpb1), and the second largest subunit of RNA polymerase II (rpb2), we inferred the divergence times for members of the Cordycipitaceae, improving the internal phylogeny of this fungal family. Molecular clock analyses indicate that the ancestor of Akanthomyces sensu lato occurred in the Paleogene period (34.57 Mya, 95% HPD: 31.41–37.67 Mya), and that most species appeared in the Neogene period. The historical biogeography of Akanthomyces sensu lato was reconstructed using reconstructing ancestral state in phylogenies (RASP) analysis, indicating that it most likely originated in Asia. Combined morphological characterization and phylogenetic analyses were used to identify and taxonomically place five species within Cordycipitaceae. These include the following: (i) two new species, namely Akanthomyces baishanensis sp. nov. and Samsoniella sanmingense sp. nov., (ii) a new record species isolated from infected Lepidopteran host, Blackwellomyces lateris, (iii) a new record species in the genus Niveomyces, with sporothrix-like asexual morphs, namely N. multisynnematus, isolated from dipteran insects (flies), and (iv) a known species of the (hyper-) mycoparasite, Liangia sinensis, isolated from the fungus Ophiocordyceps globiceps (Ophiocordycipitaceae) growing on a dipteran host. Our data provide a significant addition to the diversity, ecology, and evolutionary aspects of the Cordycipitaceae. Full article

We present a molecular phylogeny for the subtribe Ecliptinae (Asteraceae, Heliantheae) based on three plastid (matK, psbA-trnH, and trnQ-rps16) and two nuclear (nrITS and nrETS) markers. The results of the phylogenetic reconstruction were utilised as a topological constraint for a subsequent divergence dating analysis and ancestral range reconstructions. We sampled 41 species and 40 genera (72%) of Ecliptinae and two species of Montanoa (as outgroups) to elucidate the generic relationships between the genera of this subtribe. The Bayesian inference (BI) and Maximum Likelihood (ML) analyses were performed for the combined molecular dataset. The divergence dating analysis was performed using a relaxed, uncorrelated molecular clock with BEAST v1.8.4 and calibrated using a single secondary calibration point from a recently published chronogram for the family. The ancestral range reconstructions focusing on continents (i.e., South America, North America, Africa, Asia, and Oceania) and biomes (Dry forests, Altitudinal grasslands, Savannas, and Rainforests) were performed on BioGeoBEARS. Our phylogenetic results indicate that the genera of Ecliptinae are grouped into five clades, informally named the Monactis, Oblivia, Blainvillea, Wedelia, and Melanthera clades. The most recent, common ancestor of Ecliptinae was widespread in the North and South American dry forests at 8.16 Ma and mainly radiated in these regions up to the Pleistocene. At least eight dispersal events to South America and four dispersal events from North America to Africa, Asia, and Oceania took place during this period in all five informal clades of Ecliptinae. At least 13 biome shifts from dry forests to rainforests were evidenced, in addition to ten biome shifts from dry forests to altitudinal grasslands and savannas. These results corroborate the mid-late Miocene to early Pleistocene radiation of Ecliptinae in tropical dry forests. Future studies should aim to sample the remaining 14 unsampled genera of Ecliptinae to position them in one of the five informal clades proposed in this study. Full article